I did a backup of the folder software and after restarting services, i did an "update by web".

All the packages came back from internet and everything seems fine.

That will have restored the content packages, like DATs and engines - but it will not have replaced any point product packages that were checked in at install time or by you manually (for example VSE install packages, agent key updaters, and so on.)

but we've got always the same messages from clients 'File catalog.z is corrupt", strange, no ?

Unfortunately as you have noticed the agent is not able to communicate with the server... you really need to resolve this problem before anything else. I would recommend opening a case with support - there are a large number of problems that can cause this kind of failure, and it's a bit beyond the scope of this forum